HDX-MS Combining Molecular Dynamics Simulation Reveals Structural Basis of Transcriptional Coactivator PC4 Binding to a Platinum Crosslinked Double-Stranded DNA

<p>Human nuclear protein positive cofactor PC4 is a DNA-binding protein, and plays an important role in the early response to DNA damage by recognizing single-stranded oligodeoxynucleotide domain and facilitating the subsequent steps of DNA repair. Our group previously discovered that PC4 selectively binds to a double-stranded oligodeoxynucleotide (dsODN) damaged by a trans-platinum anticancer complex, trans-[PtCl2(NH3)(thiazole)] (trans-PtTz). However, the molecular basis of this unique recognition and interaction remained unclear. In this work, amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) was applied to dissect the interaction interface between PC4 and a 15-mer double-stranded oligodeoxynucleotide crosslinked by trans-PtTz (trans-PtTz-dsODN). Global deuterium uptake suggested a 1:1 binding stoichiometry of PC4 to trans-PtTz-dsODN. Local deuterium uptake revealed that the flexible N-terminal loop and the β3 – β5-sheet played key roles in the recognition and interaction between PC4 and trans-PtTz-dsODN. In order to locate the key amino acid residues, molecular dynamics simulation was employed, demonstrating that PC4 binds to the trans-PtTz-dsODN at the minor groove via strong H-bonds with the nucleobases of the complementary strand. The minor groove width was broadened to adapt for the binding of PC4. Arg86 residue in PC4 was shown to dominate the recognition and interaction, which was verified by electrophoretic mobility shift assays. This work profiles the detailed interaction mechanism of PC4 with trans-PtTz damaged dsODN, and the combination use of HDX-MS and molecular dynamics simulation provides a new paradigm for the future research of the cellular response to the platinum induced DNA damage.</p>

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Molecular Dynamics Simulation of the Influenza A(H3N2) Hemagglutinin Trimer Reveals the Structural Basis for Adaptive Evolution of the Recent Epidemic Clade 3C.2a

Frontiers in Microbiology ◽

10.3389/fmicb.2017.00584 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 12

Author(s):

Masaru Yokoyama ◽

Seiichiro Fujisaki ◽

Masayuki Shirakura ◽

Shinji Watanabe ◽

Takato Odagiri ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Adaptive Evolution ◽

Influenza A ◽

Dynamics Simulation ◽

Structural Basis

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Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site

Journal of Computational Chemistry ◽

10.1002/jcc.20184 ◽

2005 ◽

Vol 26 (8) ◽

pp. 788-798 ◽

Cited By ~ 21

Author(s):

Hirofumi Fujimoto ◽

Miroslav Pinak ◽

Toshiyuki Nemoto ◽

Peter O'Neill ◽

Etsuo Kume ◽

...

Keyword(s):

Molecular Dynamics ◽

Dna Damage ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Abasic Site ◽

Clustered Dna Damage

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Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

Canadian Journal of Chemistry ◽

10.1139/cjc-2014-0371 ◽

2015 ◽

Vol 93 (3) ◽

pp. 348-361 ◽

Cited By ~ 2

Author(s):

C. Izanloo

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Double Helix ◽

Melting Process ◽

Minor Groove ◽

Dynamics Simulation ◽

Transition Curve ◽

Water Molecules ◽

Major Groove ◽

Dna Duplex

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

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